Japan’s wild side is often lost in translation: True, where it’s urban, it’s really urban, and where it’s expensive, it’s really expensive. But we’re not talking about a business trip to Tokyo. There is an undeveloped Japan—and plenty of it. A landscape as forested as any on Earth stretches from the subtropical reefs near Okinawa to the soaring, jagged mountains of Hokkaido. It’s rugged, welcoming, and a better bargain than you might think. "Japan’s ryokans [country inns] are the best value in the world," says Duff Trimble, whose Toronto-based Wabi-Sabi Japan (wabi-sabijapan.com) runs custom guided Japan adventures. A top-notch ryokan, for about $400 per person per night, dishes up incredible service, serene rooms, communal soaks in hot springs, garden settings, and infallibly polite hosts. (Don’t ever look puzzled unless you’re willing to be aided, abetted, and maybe even escorted by legions of locals.) Simple small-town hotels run less than $100. And at mealtime, for under $20 you can fill up on sushi and other Japanese delicacies—if you like seaweed, roe, eel, and the odd giant sea snail, you’re in the right place. A seven-day rail pass on the country’s sleek 180-mph bullet trains can be had for under $300—less than half the cost of an equivalent pass in Europe. Best of all, Trimble says, "people are eager to welcome you. They’re fiercely proud of their culture, which is so closely tied to Japan’s landscape."

1. Koyasan

Make a Buddhist Pilgrimage

Arguably the holiest place in Japan, Koyasan is a complex of 117 Buddhist temples, ensconced in the cedar-forested mountains of central Japan’s Kii Peninsula. It is the home of Shingon Buddhism, where monks and pilgrims study, strive for perfect enlightenment—and happily share the experience with visitors. Koyasan is accessible by train from Osaka, but for the true spiritual journey, disembark at Kudoyama and trek there along the 14-mile Choisi Pilgrim Route, which winds past 180 five-tiered stone stupas, dating from the 13th century. Join monks for chants and prayers at early morning services, explore lush gardens, pagodas, and shrines, and don’t miss the Okunoin cemetery, final resting place of sundry samurai, kabuki actors, animals, nobility, and Kobo Daishi himself, founder of Shingon Buddhism. The only thing that might disturb your sense of serenity here is the "corporate tomb," in which professional associates were buried together—unless you like the idea of spending eternity with your co-workers.

Vitals: Hop the Nankai Electric Railway from Namba Station, in Osaka (shukubo.jp/eng). Fifty-three temples offer accommodations, called shukubo, ranging from hostel-like to zen-plush; make reservations at the Tourist Information Center ($75, including breakfast and dinner).

2. Yonaguni Jima

Dive a Lost City

"They’re a cross between the pyramids and Mayan ruins—only underwater," says scuba tour operator Lisa Slater of the stone formations off Yonaguni Jima’s coast. Discovered in 1986, the mysterious site is surrounded by controversy: Some claim it’s the handiwork of a 12,000-year-old civilization; others contend that what appear to be extensive carved megaliths, staircases, and a stone turtle statue are simply the work of natural erosion. But, Slater says, "it’s a phenomenal dive site regardless. Beautiful, warm water with a hundred feet of visibility, large drop-offs, and reef walls." Slater’s California-based Open Coast Travel runs trips there year-round, but divemaster Doug Bennett of Reef Encounters in Okinawa favors winter diving at Yonaguni, when migrating humpback whales and hammerhead sharks "spice things up a bit." Southern Japan scuba trips are best launched from Okinawa, which has great diving in its own right, with exotica such as pygmy seahorses and frogfish. And any scuba itinerary here should include Zamami, in the nearby Kerama Islands, and Ishigaki Shima; both have gently sloping reefs and a laid-back, Key West vibe that’s fun even for nondivers.

The colossal, millennia-old cedars of subtropical Yakushima island draw flocks of hikers, but most come to gawk at a single tree: 7,200-year-old Jomon-sugi, considered the oldest in Japan—if not the world. The ancient behemoth, at 83 feet tall and 50 feet wide, is certainly worth a visit, but the surrounding forest shouldn’t be missed. These gnarled trees are massive in girth, festooned with epiphytic rhododendrons and azaleas, and frequently shrouded in mist. (The locals swear it rains 370 days a year here.) Take a three-day, 18-mile traverse of rugged Yakushima, starting near Onoaida, to the north coast village of Kusugawa. A side hike on day two leads to Miyanoura-dake, the island’s 6,348-foot apex. Finish with a stay in the upscale Iwasaki Hotel, whose hot baths have cedar log floors.

Vitals: Fly from Tokyo to Kagoshima, on Kyushu island; connect to the city of Miyanoura, on Yakushima island, via Japan Air Commuter or the Toppy 2 Ferry ($80, round-trip).

4. Noto Peninsula

Pedal a Forgotten Peninsula

Precisely because urban Japan is so modern and alluring, most have forsaken rural life for the cities, leaving places like the Noto Peninsula of central Honshu to thrive unspoiled—well off the radar of tourists and locals alike. Thanks to a few sleek highways that siphon off vehicle traffic, the bucolic region is crisscrossed by smooth, quiet roads where you can tranquilly pedal past terraced rice paddies and see nary a Toyota. The Noto is a smorgasbord of great food, art, religion, scenery, and authentic accommodations: Overnight in simple hotels with tatami mat floors and futon beds; no fancy B&Bs around here. It’s possible to cycle the Noto on your own, but rental bikes are often inadequate three-speeds, and maps and road signs will be in Japanese only. Imagine that.

The brilliantly red Torii Gate, floating off the coast of Miyajima, represents the passage from reality to the realm of the spirit—a fitting symbol for the transition into the otherworldly beauty of a kayaking trip in the Seto Sea. Here hundreds of gumdrop islands dot the water, but tiny Miyajima is the gem. Maine-based H2Outfitters leads paddling excursions that circumnavigate much of the island’s 19-mile coast, nosing into sea caves and oyster farms and settling onto pocket beaches for traditional bento box lunches. Home base is a little ryokan that serves killer fried eel. Beyond the main village Miyajima is mostly wilderness. A trek to its high point, 1,739-foot Mount Misen, passes through lush forest, populated by tame deer and frisky monkeys, to magnificent Seto views. "A paddling trip is a great way to see Miyajima," says H2O’s Jeff Cooper, "and to avoid getting ‘shrined out,’ which can be easy to do in Japan."

Daisetsuzan National Park is the crowning glory of mountainous Hokkaido island. While not exactly the Rockies—the park’s conical peaks top out just above 7,500 feet—the prominent summits, deep snows, steaming fumaroles, and dense subalpine vegetation make it feel like the top of the Earth. Start in the hot-springs resort of Asahi Dake, where a cable car leads to the park’s signature ten-mile trek. Heading into the high country, pause for reflection at Sugatami-ike, a pond that mirrors the surrounding wildflowers and 7,513-foot Asahi Dake. All of Daisetsuzan is visible from its summit, including flat-topped Kurodake—your next peak to bag a few hours farther down the trail.

Vitals: Fly from Tokyo to Asahikawa, where $10 bus service is available to Asahi Dake. Overnight at Asahi Dake’s Daisetsuzan Shirakaba-so Youth Hostel, a spacious inn with outdoor hot springs ($40; youthhostel.or.jp).